The Mechanisms of Coexistence and Competitive Exclusion in Complex Plankton Ecosystem Models

The biodiversity of plankton ecosystems may no longer be a paradox, but the mechanisms that determine coexistence of explicit competitors in ecosystems remain a mystery. This is particularly so in ecosystem models, where competitive exclusion remains the dominant process. Climate and fisheries models require plankton ecosystem sub-models that maintain competing plankton functional types extant, but coexistence can be reproduced in only a few ‘just so’ theoretical models. This limits our ability to predict the impacts of climate change and fisheries on ocean biota. We consider ecosystems of Kolmogorov form that conserve mass (CK systems). These systems describe a general class of ecosystem models that includes many theoretical and applied models. We develop heuristics that illuminate the key mechanisms that allow the coexistence of explicit competitors in these systems. These heuristics facilitate the identification of a large class of models with the structural property that all species coexist for all time. Our approach unifies many theoretical and applied models in a common biogeochemical framework, providing a powerful tool with the potential to generate new insights into the properties of complex ecosystems.     

Nucleotide mutations in purA gene and pur operon promoter discovered in guanosine- and inosine-producing Bacillus subtilis strains

The promoter region of the pur operon, which contains 12 genes for inosine monophosphate biosynthesis from phosphoribosylpyrophosphate, and the purA gene, encoding the adenylosuccinate synthetase, were compared among wild-type and three purine-producing Bacillus subtilis strains. A single nucleotide deletion at position 55 (relative to translation start site) in purA gene was found in a high inosine-producing strain and in a high guanosine-producing strain, which correlates with the absence of adenylosuccinate synthetase activity in these strains. Within the pur operon promoter of high guanosine-producing strain, in addition to a single nucleotide deletion in PurBox1 and a single nucleotide substitution in PurBox2, there were 4 substitutions in the flanking region of the PurBoxes and 32 nucleotide mutations in the 5′ untranslated region. These mutations may explain the purine accumulation in purine-producing strains and be helpful to the rational design of high-yield recombinant strains.     

Competition of two suspension-feeding protozoan populations for a growing bacterial population in continuous culture

Mathematical studies for ecosystems involving 2 predators competing for a growing prey population have shown that the 2 competitors can coexist in a state of sustained oscillations for a range of values of the system parameters. For the case of 1 suspension-feeding protozoan population, recent experimental observations suggest that the predator-prey interaction is complicated by the ability of the bacteria to grow on products produced by the lysis of protozoan cells. This situation is studied here for the case where 2 suspension-feeding protozoan populations compete for a growing bacterial population in a chemostat. Computer simulations show that the 2 protozoan populations can coexist over a range of the operating parameters. Some necessary conditions for coexistence are presented as are some speculations regarding the possible physical explanations of results.     

Genetic and molecular events in transformation ofHaemophilus influenzae with plasmid RSF 0885 carrying cloned segments of chromosomal DNA

InHaemophilus influenzae genetic transformation for a plasmid marker is significantly increased when recombinant plasmid RSF 0885 DNA carrying chromosomal DNA segments is used instead of the plasmid DNA alone. Chromosomal DNA by itself, added even a few minutes after the addition of plasmid DNA to competent cells, stopped further uptake of the plasmid DNA. These observations are consistent with the idea that plasmid RSF 0885 contains a ‘degenerate’ version of the required eleven base-pair ‘uptake sequence’ inHaemophilus. The transformation activity of the recombinant plasmid DNA is recoverable after its entry into cells, although the specific biological activity of the re-isolated plasmid DNA is less than that of the parental recombinant plasmid DNA. Therec 1 gene function of the host is necessary for obtaining higher transformation frequencies with recombinant DNA from five different clones. The reduced transformation frequencies seen inrec 1 ^- strain is not all due to a permanent damage to the donor DNA since the recovered recombinant plasmid DNA from such cells can increase the transformation efficiency onrec 1 ⁺ strain.     

Bacterial competition in serial transfer culture

A mathematical model of bacterial competition for a single growth-limiting substrate in serial transfer culture is formulated. Each bacterial strain is characterized by a growth response function, e.g. Monod function determined by a maximum growth rate and half-saturation nutrient concentration, and the length of its lag phase following the dilution event. The goal of our study is to understand what factors determine an organisms fitness or competitive ability in serial transfer culture. A motivating question is: how many strains can coexist in serial transfer culture? Unlike competition in the chemostat, coexistence of two strains can occur in serial transfer culture. Numerical simulations suggest that more than two may coexist.     

Comparison of growth and lipid content in three <Emphasis Type="Italic">Botryococcus braunii</Emphasis> strains

The growth and lipid content of three Botryococcus braunii strains from China (CHN), United Kingdom (UK) and Japan (JAP) were compared at three temperatures (20, 25 and 30 ^∘C), three irradiances (60, 100 and 300 W m⁻²) and four salinities (0, 0.15, 0.25, and 0.5 M NaCl) for 30 days, respectively. In the temperature trial, the UK strain and JAP strain grew faster at 25 ^∘C than at other temperatures, while the CHN strain performed equally well at 20 and 25 ^∘C. The JAP strain grew slowest among the three strains at all temperatures, whereas the growth rate of the CHN and UK strains was similar at all temperatures except at 20 ^∘C. The UK strain contained the highest lipid content, but the CHN strain had the lowest lipid content at most temperatures. In the light trial, the highest growth rate was found in the UK strain and the lowest growth rate was observed in the JAP strain at most irradiances. The UK and JAP strains contained more lipids than the CHN strain at 60 and 100 W m⁻², but the lipid content was not significantly different among the three strains at 300 W m⁻². In the salinity trial, both the CHN and UK strains grew faster than the JAP strain at all salinities, but the growth rate between the CHN and UK strains was not different. However, the CHN strain had the lowest lipid content whereas the UK strain produced the highest lipids at most salinities. Our results indicate that the CHN strain and the UK strain grow faster than the JAP strain, but the UK and JAP strains produce more lipids than the CHN strain. The UK strain should be considered as a potential B. braunii strain for the exploitation of renewable energy.     

Competition of two microbial populations for a single resource in a chemostat when one of them exhibits wall attachment

It is known that two microbial populations competing for a single resource in a homogeneous environment with time-invariant inputs cannot coexist in a steady state. The case where two microbial populations compete for a single resource in a chemostat but one of them exhibits attachment to the chemostat walls is studied theoretically. Because of the cells' attachment to the walls, the environment is no longer homogeneous. The present article considers the case where the attached cells form no more than a monolayer. Other situations occur, often frequently, but we do not consider them here. Two models are used to represent the attachment to the walls: the Topiwala-Hamer model and a model which assumes that the attachment of microbial cells to the solid surfaces is a reversible process. The first model does not allow the population that exhibits wall attachment to wash out from the chemostat, in contrast to the second model (which nevertheless reduces to the first one in the limit). It has been found that in most of the possible cases for both models, the two competitors can coexist in a stable steady state for a wide range of the operating parameters space. The results of the stability analysis are discussed and analytical expressions for the conditions and the boundaries of the domains of stable coexistence are given for all the possible situations that may arise.     

The effects of wall populations on coexistence of bacteria in the liquid phase of chemostat cultures

We have examined the effects of wall populations on coexistence between strains of Escherichia coli in the liquid phase of mixed (two-strain) chemostats. The wall populations of the two competing strains became established soon after the start of the cultures and, although the relative abundance of the strains in the liquid phase could change over time by several orders of magnitude, the composition of an established wall population did not change markedly. The bacterial strains examined could not displace an established wall population of a competing strain. The presence of a permanent wall population allowed a strain that was less fit in the liquid phase to coexist with a superior strain. The resulting coexistence did not require that the inferior strain attached to the vessel wall better than the superior strain. We believe that the coexistence developed because the inferior strain survived and reproduced on the vessel wall. The progeny from that wall population then provided replacements for the bacteria that the inferior strain lost through a selective disadvantage in the liquid phase of the culture. By replacing the chemostat vessel, hence eliminating the wall populations, we could distinguish between cases where the coexistence depended on the presence of a wall population and where it resulted from some alternative mechanism.     

Kinetics of plasmid transfer among <Emphasis Type="Italic">Bacillus cereus </Emphasis>group strains within lepidopteran larvae

The cry toxin encoding plasmid pHT73 was transferred from Bacillus thuringiensis subspecies kurstaki KT0 to six B. cereus group strains in three lepidopteran (Spodoptera exigua, Plutella xyllostella and Helicoverpa armigera) larvae by conjugation. The conjugation kinetics of the plasmid was precisely studied during the larval infection using a new protocol. The infections were performed with both vegetative and sporulated strains. However, larval death only occurred when infections were made with spore and toxin preparations. Likewise, spore germinations of both donor and recipient strains were only observed in killed larvae, 44–56 h post-infection. Accordingly, kinetics showed that gene transfer between B. thuringiensis strain KT0 and other B. cereus strains only took place in dead larvae among vegetatively growing bacteria. The conjugational transfer ratios varied among different strain combinations and different larvae. The highest transfer ratio reached 5.83 × 10⁻⁶ CFU/donor between the KT0 and the AW05R recipient in Helicoverpa armigera, and all transconjugants gained the ability to produce the insecticidal crystal. These results indicated that horizontal gene transfer among B. cereus group strains might play a key role for the acquisition of extra plasmids and evolution of these strains in toxin susceptible insect larvae.     

Chromosome-shuffling technique for selected chromosomal segments in Saccharomyces cerevisiae

We describe a novel chromosome engineering technique for shuffling selected regions of chromosomes from two strains in Saccharomyces cerevisiae: The technique starts with the construction of MAT a and MATα strains in which a particular chromosome is split at exactly the same site in both strains such that the split chromosomes generated are marked with different markers. The two strains are then crossed, and the resultant diploid is cultivated in nutrient medium to induce loss of the split chromosome originating from either of the strains. We predicted that some of these clones that are hemizygous for the split chromosome would spontaneously restore a homozygous configuration of the split chromosome during cultivation. We verified this prediction by tetrad analysis and quantitative Southern hybridization analysis, indicating that it is possible to create diploid hybrids in which a selected region of a chromosome from one strain is replaced by the corresponding chromosomal region from another strain. We also found that some chromosomal segments maintain a hemizygous state. This novel technique, which we call ‘chromosome shuffling’, could provide a new tool to analyze phenotypic alterations caused by the replacement or hemizygosity of a selected chromosomal region in not only laboratory but also industrial strains of S. cerevisiae.     

Physiological characteristics and competitive ability of plasmid-cured derivatives of Rhizobium fredii USDA 206

Rhizobium fredii USDA 206 carries four plasmids which total more than 1200 MDa of DNA. A series of plasmid-cured mutants of strain USDA 206 were derived and compared to determine possible functions of the plasmids, as well as the effect of the plasmids on growth and competitiveness of their host strains. No functions of plasmid pRj206a or pRj206c were found. Plasmid pRj206b was found to have a higher copy number in the non-mucoid (Muc^–) derivative strain 206CANS. Transfer of pRj206b conferred on two recipient strains a Muc^– phenotype indicating control of exopolysaccharide synthesis by this plasmid. The same plasmid appeared to encode repression of melanin synthesis. Strain 206CANS was also shown to have a shorter generation time than USDA 206 and to out-compete USDA 206 in batch and chemostat culture. Competition for nodulation indicated little difference between USDA 206 and 206CANS, while USDA 206 appeared to be more competitive than two of the other cured derivatives.Paper no. 11886 of the Journal Series of North Carolina Agricultural Research Service, Raleigh, NC 27695-7643. Cooperative investigations of the U.S. Department of Agricultural, Agricultural Research Service and the North Carolina Agricultural Research Service Raleigh, NC 27695-7601, USA     

Niche diversity in crustacean cryptic species: complementarity in spatial distribution and predation risk

Recent genetic studies indicate that species with very close phenotypic similarity (“cryptic species”) are a common feature of nature, and that such cryptic species often coexist in communities. Because traditional views of species coexistence demand that species differ in phenotype to coexist stably, the existence of sympatric cryptic species appears to challenge traditional perspectives of coexistence. We evaluated niche diversity in three recently discovered species of Hyalella amphipods that occur sympatrically in lakes and share close phenotypic similarity. We found that, in some cases, these species exhibited strong complementary spatial distributions within the littoral zone of lakes, both across a distance-from-shore gradient, and a vertical depth gradient. Additionally, we compared fish stomach contents with habitat samples and found that species differed in their vulnerability to predation from sunfish (Lepomis spp.). Complementarity among species across axes of spatial distribution and predation risk, two important niche components, suggests that species with close phenotypic similarity may differ appreciably along ecologically relevant axes. Our results, considered in the light of previous studies, suggest a community structured by predator-mediated coexistence or sequential dominance across environmental gradients in the littoral zone.     

Integration of minitransposons for expression of the Escherichia coli elt genes at a preferred site in Salmonella typhimurium identifies a novel putative fimbrial locus

An asd-complementing mini-Tn5 transposon was constructed for random insertion of the Escherichia coli LT enterotoxin genes (elt) into the genome of Δasd attenuated strains of Salmonella typhimurium. Transfer of the minitransposon to different S. typhimurium strains resulted in random integration only in strain χ4072, while in strain χ3987, which harbours the virulence plasmid, over 20% of the insertions occurred at the same site. Expression of elt was found to be highest in Salmonella isolates carrying the mini-Tn5 integrated at the preferred site, which was mapped to an uncharacterised region of the virulence plasmid. Sequence analysis of the integration site showed that it lies within an open reading frame with sequence similarity to E. coli leuO and contiguous to a novel fimbrial locus. Received: 26 August 1998 / Accepted: 9 November 1998     

A kinetic study on the plasmid stability of three <Emphasis Type="Italic">Lactococcus lactis</Emphasis> strains

Absract The plasmid stability of three wild type Lactococcus lactis strains and their mutants was investigated at different incubation time and temperatures in two different media [M17 broth and reconstituted skim milk (RSM)]. The results showed that both incubation times and temperature are effective on plasmid loss. The plasmid profiles of wild type strains exhibited 8 to 9 distinct plasmid species with molecular weights from 2.1 to 24.0 kb. Lactose fermentation ability was found to be encoded by 22.2 (strain U70), 23.6 (strain U29) and 24.0 (strain U52) kb plasmids in the wild type strains, respectively. The stabilities of the plasmids were explained by applying a second-order polynomial modeling system. Reasonable fittings were obtained for the model and the adjusted regression coefficients (R ² _adj) were between 0.76 and 0.99 for the overall data. Overall, it was found that incubation time had the most profound effect on plasmid stability, with plasmid loss occurring after 72 h, while temperatures in the range of 15–40°C also induced plasmid instability.     

Inulinase-hyperproducing strains of Kluyveromyces sp. isolated from aguamiel (Agave sap) and pulque

Summary Two strains of Kluyveromyces marxianus (A1 and A2) isolated from ‘aguamiel’ (agave sap) and one strain of K. lactis var. lactis (P7) isolated from ‘pulque’ (its fermented product), were studied to make a survey of inulinase production. The strains of K. marxianus A1 and A2 were the best producers of inulinase, giving up to 2.5 times more enzyme than the control hyperproducing strain K. marxianus CDBB-L-278, and showed lower catabolic repression than this. One strain isolated from pulque was identified as K. lactis var. lactis and was also an excellent inulinase producer, being the first strain of this species reported as such. These strains were very good inulinase producers and they had low susceptibility to catabolic repression probably because the source from which they were isolated was rich in sucrose and oligofructans. They can be used in the transformation of inulin to produce fructose and/or oligofructans.     

Effects of medium composition and nutrient limitation on loss of the recombinant plasmid pLG669-z and β -galactosidase expression by Saccharomyces cerevisiae

The effects of medium composition, nutrient limitation and dilution rate on the loss of the recombinant plasmid pLG669-z and plasmid-borne β -galactosidase expression were studied in batch and chemostat cultures of Saccharomyces cerevisiae strain CGpLG. The difference in growth rates between plasmid-free and plasmid-containing cells (Δμ) and the rate of segregation (R) were determined and some common factors resulting from the effect of medium composition on plasmid loss were identified. Glucose-limited chemostat cultures of CGpLG grown on defined medium were more stable at higher dilution rates and exhibited Δμ -dominated plasmid loss kinetics. Similar cultures grown on complex medium were more stable at lower dilution rates and exhibited R-dominated plasmid loss kinetics. Overall plasmid stability was greatest in phosphate-limited chemostat cultures grown on defined medium and was least stable in magnesium-limited cultures grown on defined medium. Δμ decreased and R increased with increased dilution rate, irrespective of medium composition. Increased plasmid loss rates at high or low dilution rates would appear to be characteristic of loss kinetics dominated by R or Δμ, respectively. Growth of glucose-limited chemostat cultures on complex medium decreased Δμ values but increased R values, in comparison to those cultures grown on defined medium. Any increased stability that a complex medium-induced reduction of Δμ may have conferred was counteracted by an increased R value. Increased β-galactosidase productivity was correlated with increased plasmid stability only in glucose-limited chemostat cultures grown on defined medium and not in those grown on complex medium. Previous studies have yielded contrasting responses with regard to the effect of dilution rate on recombinant plasmid loss from S. cerevisiae. Our findings can account for these differences and may be generally valid for the stability of similar yeast plasmid constructs. This information would facilitate the design of bioprocesses, where recombinant plasmid instability results in reduced culture productivity. Received 08 July 1996/ Accepted in revised form 14 January 1997     

Induction and derepression of arginase and ornithine transaminase in different strains ofSaccharomyces cerevisiae

The syntheses of arginase and ornithine transaminase were studied in two strains ofSaccharomyces cerevisiae, viz. strain B and strain α-Σ1278b. Derepression of both enzymes during nitrogen starvation was shown only by strain B, non-specific induction of arginase only by strain α-Σ1278b. This different response of both strains studied reveals substantial differences in the regulation of enzyme synthesis among yeast strains of one and the same species. The specific enzyme activities observed in chemostat cultures with arginine as the nitrogen source and different sugars, at variable carbon to nitrogen ratios, did not indicate the involvement of carbon catabolite repression in the regulation of arginase and ornithine transaminase syntheses. Specific arginase activities observed in the continuous cultures varied widely and did not show a correlation with the intracellular arginine concentration. Extracellular steady-state arginine concentrations higher than about 0.1mm, in addition to abundant energy supply, were found to be required for high production of arginase. It is suggested that, besides intracellular arginine, extracellular arginine may provide an induction signal necessary for full-scale induction of arginase synthesis. A possible intermediary role of arginine permeases or of other membrane proteins is discussed.     

Analysis of the tellurite resistance determinant on the pNT3B derivative of the pTE53 plasmid from uropathogenic Escherichia coli

We have found and sequenced a significant part of the previously described tellurite resistance determinant on mini-Mu derivative pPR46, named pNT3B, originally cloned from a large conjugative plasmid pTE53, found in Escherichia coli. This plasmid contains genes essential for tellurite resistance, together with the protective region bearing genes terX, Y, W, and the conserved spacing region bearing several ORFs of unknown function. Computer analysis of obtained sequence revealed a close similarity to the formerly described ter operons found on the Serratia marcescens plasmid R478 and the chromosome of Escherichia coli O157:H7. This finding confirms the presence of a whole region on the large conjugative plasmid that pTE53 originated from a uropathogenic E. coli strain, and suggests its possible role in horizontal gene transfer, resulting in the development of new pathogenic E. coli strains.     

Competition of plasmid-bearing Pseudomonas putida strains catabolizing naphthalene via various pathways in chemostat culture

Plasmid-carrying Pseudomonas putida strains degrade naphthalene through different biochemical pathways. The influence of various combinations of host bacteria and plasmids on growth characteristics and competitiveness of P. putida strains was studied in chemostat culture at a low dilution rate (D=0.05 h⁻¹) with naphthalene as the sole source of carbon and energy. Under naphthalene limitation, the plasmid-bearing strains degrading naphthalene that use catechol 1,2-dioxygenase for catechol oxidation (ortho pathway), were the most competitive. The strains bearing plasmids that control naphthalene catabolism via catechol 2,3-dioxygenase (meta pathway), were less competitive. Under these conditions the strain carrying plasmid pBS4, which encodes for naphthalene catabolism via gentisic acid, was the least competitive. Received: 24 February 1997 / Received revision: 22 May 1997 / Accepted: 25 May 1997     

Toluene biodegradation by <Emphasis Type="Italic">Pseudomonas putida</Emphasis> F1: targeting culture stability in long-term operation

The stability of Pseudomonas putida F1, a strain harbouring the genes responsible for toluene degradation in the chromosome was evaluated in a bioscrubber under high toluene loadings and nitrogen limiting conditions at two dilution rates (0.11 and 0.27 h⁻¹). Each experiment was run for 30 days, period long enough for microbial instability to occur considering previously reported studies carried out with bacterial strains encoding the catabolic genes in the TOL plasmid. At all tested conditions, P. putida F1 exhibited stable performance as shown by the constant values of the specific toluene degradation yield, CO₂ produced versus toluene degraded yield, and biomass concentration within each steady state. Benzyl alcohol, a curing agent causing TOL plasmid deletion in Pseudomonas strains, was present in the cultivation medium as a result of the monooxygenation of toluene by the diooxygenase system of P. putida F1. However, no mutant population growing at the expense of the extracellular excreted carbon or lysis products was established in the chemostat as confirmed by the constant dissolved total organic carbon (TOC) concentration and fraction of toluene degrading cells (approx. 100%). In addition, batch experiments conducted with both lysis substrate and toluene simultaneously confirmed that P. putida F1 preferentially consumed toluene rather than extracellular excreted carbon.